meta-edc 1.0.0__tar.gz → 1.0.2__tar.gz

{meta_edc-1.0.0 → meta_edc-1.0.2}/CHANGES

@@ -1,6 +1,11 @@
 Changes
 -------
 
+1.0.1
+-----
+- add subject transfer action to parent list of offschedule actions.
+  Fixes exception raised when taking a transferred subject off schedule.
+
 1.0.0
 -----
 - bump edc 1.0.0

{meta_edc-1.0.0 → meta_edc-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: meta-edc
-Version: 1.0.0
+Version: 1.0.2
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt

{meta_edc-1.0.0 → meta_edc-1.0.2}/meta_edc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: meta-edc
-Version: 1.0.0
+Version: 1.0.2
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt

{meta_edc-1.0.0 → meta_edc-1.0.2}/meta_edc.egg-info/SOURCES.txt

@@ -547,6 +547,7 @@ meta_prn/tests/urls.py
 meta_prn/tests/tests/__init__.py
 meta_prn/tests/tests/test_actions.py
 meta_prn/tests/tests/test_dm_referral.py
+meta_prn/tests/tests/test_eos_events.py
 meta_prn/tests/tests/test_manager_order.py
 meta_prn/tests/tests/test_pregnancy_notification.py
 meta_rando/__init__.py

{meta_edc-1.0.0 → meta_edc-1.0.2}/meta_prn/action_items.py

@@ -43,6 +43,7 @@ class OffscheduleAction(ActionWithNotification):
         DEATH_REPORT_ACTION,
         LTFU_ACTION,
         BLOOD_RESULTS_RFT_ACTION,
+        SUBJECT_TRANSFER_ACTION,
     ]
     reference_model = "meta_prn.offschedule"
     show_link_to_changelist = True
@@ -72,6 +73,7 @@ class OffschedulePregnancyAction(ActionWithNotification):
         UNBLINDING_REVIEW_ACTION,
         DEATH_REPORT_ACTION,
         LTFU_ACTION,
+        SUBJECT_TRANSFER_ACTION,
         DELIVERY_ACTION,
     ]
     reference_model = "meta_prn.offschedulepregnancy"
@@ -85,6 +87,27 @@ class OffschedulePregnancyAction(ActionWithNotification):
         return next_actions
 
 
+class OffscheduleDmReferralAction(ActionWithNotification):
+    name = OFFSCHEDULE_DM_REFERRAL_ACTION
+    display_name = "Submit Off-Schedule (Diabetes Referral)"
+    notification_display_name = "Off-Schedule (Diabetes Referral)"
+    parent_action_names = [
+        DM_FOLLOWUP_ACTION,
+        DEATH_REPORT_ACTION,
+        LTFU_ACTION,
+        SUBJECT_TRANSFER_ACTION,
+    ]
+    reference_model = "meta_prn.offscheduledmreferral"
+    show_link_to_changelist = True
+    admin_site_name = "meta_prn_admin"
+    priority = HIGH_PRIORITY
+    singleton = True
+
+    def get_next_actions(self):
+        next_actions = [END_OF_STUDY_ACTION]
+        return next_actions
+
+
 class EndOfStudyAction(ActionWithNotification):
     name = END_OF_STUDY_ACTION
     display_name = "Submit End of Study Report"
@@ -150,22 +173,6 @@ class DmReferralAction(ActionWithNotification):
         return next_actions
 
 
-class OffscheduleDmReferralAction(ActionWithNotification):
-    name = OFFSCHEDULE_DM_REFERRAL_ACTION
-    display_name = "Submit Off-Schedule (Diabetes Referral)"
-    notification_display_name = "Off-Schedule (Diabetes Referral)"
-    parent_action_names = [DM_FOLLOWUP_ACTION]
-    reference_model = "meta_prn.offscheduledmreferral"
-    show_link_to_changelist = True
-    admin_site_name = "meta_prn_admin"
-    priority = HIGH_PRIORITY
-    singleton = True
-
-    def get_next_actions(self):
-        next_actions = [END_OF_STUDY_ACTION]
-        return next_actions
-
-
 class OffStudyMedicationAction(ActionWithNotification):
     name = OFFSTUDY_MEDICATION_ACTION
     display_name = "Withdrawal Study Medication"

{meta_edc-1.0.0 → meta_edc-1.0.2}/meta_prn/choices.py

@@ -2,6 +2,9 @@ from edc_constants.constants import NOT_APPLICABLE, OTHER, PATIENT, PREGNANCY, U
 
 from .constants import CLINICIAN, INVESTIGATOR, REFERRAL, SAE
 
+# from edc_transfer.constants import TRANSFERRED
+
+
 CLINICAL_WITHDRAWAL_REASONS = (
     ("kidney_disease", "Development of chronic kidney disease"),
     ("liver_disease", "Development of chronic liver disease"),
@@ -96,6 +99,7 @@ WITHDRAWAL_STUDY_MEDICATION_REASONS = (
     ),
     (INVESTIGATOR, " Investigator decision"),
     (REFERRAL, "Referral to Diabetes clinic"),
+    # (TRANSFERRED, "Patient decision to transfer out of catchment area"),
     (PATIENT, "Patient decision"),
     (OTHER, "Other reason (specify below)"),
 )

meta_edc-1.0.2/meta_prn/tests/tests/test_eos_events.py

@@ -0,0 +1,134 @@
+from django.test import TestCase
+from edc_action_item.models import ActionItem
+from edc_constants.constants import FEMALE, NEW, PATIENT, YES
+from edc_offstudy.constants import END_OF_STUDY_ACTION
+from edc_pharmacy.models import Medication
+from edc_transfer.constants import SUBJECT_TRANSFER_ACTION, TRANSFERRED
+from edc_utils import get_utcnow
+from edc_visit_schedule.constants import OFFSCHEDULE_ACTION
+
+from meta_lists.models import OffstudyReasons, TransferReasons
+from meta_pharmacy.constants import METFORMIN
+from meta_prn.action_items import OffscheduleAction, SubjectTransferAction
+from meta_prn.constants import OFFSTUDY_MEDICATION_ACTION
+from meta_prn.models import EndOfStudy, OffSchedule, OffStudyMedication, SubjectTransfer
+from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
+
+
+class TestEosEvents(MetaTestCaseMixin, TestCase):
+    def setUp(self):
+        super().setUp()
+        self.subject_screening = self.get_subject_screening(gender=FEMALE)
+        self.subject_consent = self.get_subject_consent(self.subject_screening)
+        self.subject_visit = self.get_subject_visit(
+            subject_screening=self.subject_screening,
+            subject_consent=self.subject_consent,
+        )
+        self.data = dict(
+            subject_visit=self.subject_visit.pk,
+            report_datetime=self.subject_visit.report_datetime,
+        )
+
+    def test_transfer_to_offschedule_in_order(self):
+        SubjectTransferAction(
+            subject_identifier=self.subject_consent.subject_identifier,
+            skip_get_current_site=True,
+            site_id=self.subject_consent.site_id,
+        )
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [SUBJECT_TRANSFER_ACTION])
+
+        # add a subject transfer object, which triggers next action item
+        transfer_reason = TransferReasons.objects.get(name="moved")
+        subject_transfer = SubjectTransfer.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            initiated_by="patient",
+            may_return=YES,
+            may_contact=YES,
+        )
+        subject_transfer.transfer_reason.add(transfer_reason)
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [OFFSCHEDULE_ACTION, OFFSTUDY_MEDICATION_ACTION])
+
+        OffSchedule.objects.create(subject_identifier=self.subject_consent.subject_identifier)
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [OFFSTUDY_MEDICATION_ACTION])
+
+        offstudy_rx = OffStudyMedication.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            stop_date=get_utcnow().date(),
+            last_dose_date=get_utcnow().date(),
+            reason=PATIENT,
+        )
+        offstudy_rx.medications.add(Medication.objects.get(name=METFORMIN))
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [END_OF_STUDY_ACTION])
+
+        EndOfStudy.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            last_seen_date=get_utcnow().date(),
+            offstudy_reason=OffstudyReasons.objects.get(name=TRANSFERRED),
+        )
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [])
+
+    def test_transfer_to_offschedule_raises(self):
+
+        OffscheduleAction(
+            subject_identifier=self.subject_consent.subject_identifier,
+            skip_get_current_site=True,
+            site_id=self.subject_consent.site_id,
+        )
+
+        OffSchedule.objects.create(subject_identifier=self.subject_consent.subject_identifier)
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [OFFSTUDY_MEDICATION_ACTION])
+
+        offstudy_rx = OffStudyMedication.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            stop_date=get_utcnow().date(),
+            last_dose_date=get_utcnow().date(),
+            reason=PATIENT,
+        )
+        offstudy_rx.medications.add(Medication.objects.get(name=METFORMIN))
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [END_OF_STUDY_ACTION])
+
+        EndOfStudy.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            last_seen_date=get_utcnow().date(),
+            offstudy_reason=OffstudyReasons.objects.get(name=TRANSFERRED),
+        )
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [])

{meta_edc-1.0.0 → meta_edc-1.0.2}/meta_reports/admin/last_imp_refill_admin.py

@@ -1,3 +1,4 @@
+import pandas as pd
 from django.contrib import admin, messages
 from django.core.exceptions import FieldDoesNotExist
 from django.db import models
@@ -42,14 +43,24 @@ def update_report(modeladmin, request, queryset):
             modeladmin.model(
                 subject_identifier=row["subject_identifier"],
                 site_id=row["site_id"],
-                imp_visit_date=row["imp_visit_date"],
+                imp_visit_date=(
+                    None if pd.isna(row["imp_visit_date"]) else row["imp_visit_date"]
+                ),
                 imp_visit_code=row["imp_visit_code"],
-                next_appt_date=row["next_appt_datetime"],
-                next_visit_code=row["next_visit_code"],
+                next_appt_date=(
+                    None if pd.isna(row["next_appt_datetime"]) else row["next_appt_datetime"]
+                ),
+                next_visit_code=(
+                    None if pd.isna(row["next_visit_code"]) else row["next_visit_code"]
+                ),
                 days_since=row["days_since"].days,
-                days_until=row["days_until"].days,
-                visit_code=str(int(row["imp_visit_code"])),
-                visit_code_sequence=row["imp_visit_code"] % 1,
+                days_until=None if pd.isna(row["days_until"]) else row["days_until"].days,
+                visit_code=(
+                    None if pd.isna(row["imp_visit_code"]) else str(int(row["imp_visit_code"]))
+                ),
+                visit_code_sequence=(
+                    None if pd.isna(row["imp_visit_code"]) else row["imp_visit_code"] % 1
+                ),
                 report_model=modeladmin.model._meta.label_lower,
                 created=now,
             )